I've often wondered that, and even assumed it was true, but sometimes they'd encounter oncoming traffic, so I'm not 100% sure.
It does often depend on the challenge of the episode, sometimes when they're just flogging a new Aston around the country roads of england they dont have traffic stopped, but when they take out supercars for one of these types of "greatest road" challenges (stelvio pass, transfagaslwkjfgghdsf highway) they definitely had the roads blocked off. someone earlier mentioned that the US National Parks Service controls the Blue Ridge Parkway, and given their environmental leanings and boringness, i can see how top gear might have been unable to get permission, too bad really because If they had had the opportunity, I know it would have made for some amazing driving (and hey, we americans dont always follow the speed limits...)